The present invention relates to SH3 binding peptides having a broad range of binding specificities. That is, certain members of the SH3 binding peptides disclosed bind with approximately the same facility with SH3 domains derived from different SH3 domain-containing proteins. Other members, in contrast, bind with a much greater degree of affinity for specific SH3 domains. The SH3 binding peptides are obtained from random peptide libraries that are also phage-displayed. Methods are described of obtaining the phage clones that bind to the SH3 domain targets and of determining their relevant nucleotide sequences and consequent primary amino acid sequence of the binding peptides. The resulting SH3 binding proteins are useful in a number of ways, including, but not limited to, providing a method of modulating signal transduction pathways at the cellular level, of modulating oncogenic protein activity or of providing lead compounds for development of drugs with the ability to modulate broad classes, as well as specific classes, of proteins involved in signal transduction.
2.1. Src and the 8H3 Domain
Among a number of proteins involved in eukaryotic cell signaling, there is a common sequence motif called the SH3 domain. It is 50-70 amino acids in length, moderately conserved in primary structure, and can be present from one to several times in a large number of proteins involved in signal transduction and in cytoskeletal proteins.
The protein pp60c-src represents a family of at least nine non-receptor protein tyrosine kinases (NR-PTKs). Members of this family share an overall structural organization comprising a series of catalytic and non-catalytic domains. In Src, a 14-amino-acid myristylation signal resides at the extreme amino-terminus, and is followed by a unique region that is not highly conserved among family members. Following this region are two highly conserved 60- and 100-amino-acid regions, the Src homology (SH) domains 3 and 2, respectively. SH2 and SH3 domains have been shown to play an important role in mediating protein-protein interactions in a variety of signaling pathways. Koch, C. A., et al., in Science (1991) 252:668-74. The carboxy-terminal half of Src contains the PTK catalytic domain, as well as a negative regulatory tyrosine (Y527) near the carboxy terminus. Phosphorylation of this residue (e.g., by Csk) results in the inhibition of PTK activity. Cooper, J. A., et al., in Science (1986) 231:1431-1434. Mutation of Y527- greater than F generates forms of Src with increased PTK and oncogenic activity. Cartwright, C. A., et al., in Cell (1987) 49:83-91; Kmiecik, T. E., et al., in Cell (1987) 49:65-73; and Piwicna-Worms, H., et al., in Cell (1987) 75-82.
The fact that some mutations which result in increased Src PTK and transforming activity map to the Src SH2 (Seidel-Dugan, C., et al., in Mol. Cell. Biol. (1992) 12:1835-45; and Hirai, H. and Varmus, H. E. in Mol. Cell. Biol. (1990) 10:1307-1318) and SH3 domains (Seidel-Dugan, C., et al., supra; Hirai, H. and Varmus, H. E., supra; Superti-Furga, G., et al., in Embo. J. (1993) 12:2625-34; and Potts, W. M., et al., in Oncogene Res. (1988) 3:343-355) suggests a negative regulatory role for these domains. That phosphotyrosine residues within specific sequence contexts represent high affinity ligands for SH2 domains suggests a model in which the SH2 domain participates in Y527-mediated inhibition of PTK activity by binding phosphorylated Y527, thereby locking the kinase domain in an inactive configuration. Matsuda, M., Mayer, B. J., et al., in Science (1990) 248:1537-1539. This model is supported by the observation that phosphopeptides corresponding to the carboxy-terminal tail of Src bind active, but not inactive, variants of Src. Roussel, R. R., et al., in Proc. Natl. Acad. Sci. U S A (1991) 88:10696-700; and Liu, X., et al., in Oncogene (1993) 8:1119-1126.
The mechanism of SH3-mediated inhibition of Src PTK activity remains unclear. There is evidence that pY527-mediated inhibition of Src PTK activity involves the SH3 domain as well as the SH2 domain. Okada, M., Howell, et al., in J. Biol. Chem. (1993) 268:18070-5; Murphy, S. M., et al., in Mol. Cell. Biol. (1993) 13:5290-300; and Superti-Furga, G., et al., supra. Although these effects are thought to be a consequence of SH3-mediated protein-protein interactions, precisely how the Src SH3 domain exerts its negative regulatory effect is unclear. Identification of high affinity ligands for the Src SH3 domain could help resolve these issues.
2.2. Protein Tyrosine Kinases and The Immune Response
Src-related tyrosine kinases are expressed in a variety of cell types including those of the immune system (lymphocytes, T cells, B cells, and natural killer cells) and the central nervous system (neural cells, neurons, oligodendrocytes, parts of the cerebellum, and the like). Umemori, H. et al., in Brain Res. Mol. Brain Res. (1992) Dec. 16(3-4):303-310. Their presence in these cells and tissues and their interaction with specific cell surface receptors and immunomodulatory proteins (such as T cell antigen receptor, CD14, CD2, CD4, CD40 or CD45) suggest that these kinases serve an important role in the signalling pathways of not only the central nervous system but of the immune system, as well. See, e.g., Ren, C. L. et al., in J. Exp. Med. (1994) 179(2):673-680 (signal transduction via CD40 involves activation of Lyn kinase); Donovan, J. A. and Koretzky, G. A., in J. Am. Soc. Nephrol. (1993) 4(4):976-985 (CD45, the immune response, and regulation of Lck and Fyn kinases); and Carmo, A. M. et al., in Eur. J. Immunol. (1993) 23(9):2196-2201 (physical association of the cytoplasmic domain of CD2 with p56lck and p59fyn).
For instance, mice with disruptions in their Src-like genes, Hck and Fgr, possess macrophages with impaired phagocytic activity or exhibit a novel immunodeficiency characterized by an increased susceptibility to infection with Listeria monocytogenes. Lowell, C. A. et al., in Genes Dev. (1994) 8(4):387-398. Also, it has been shown that bacterial lipopolysaccharide (LPS) activates CD14-associated p56lyn, p68hck, and p59c-fgr, while inducing the production of lymphokines, such as TNF-alpha, IL-1, IL-6, and IL-8. Inhibition of the protein tyrosine kinases blocks production of TNF-alpha and IL-1.
2.3. SH3 Binding Peptides
As mentioned above, it has long been suspected that SH3 domains are sites of protein-protein interaction, but it has been unclear what SH3 domains actually bind. Efforts to identify ligands for SH3 domains have led to the characterization of a number of SH3-binding proteins, including 3BP1 and 2 (Ren, R., Mayer, et al., in Science (1993) 259:1157-61), SOS (Olivier, J. P., et al., in Cell (1993) 73:179-91; and Rozakis-Adcock, M., et al., in Nature (1993) 363:83-5), p85 PI-3xe2x80x2 Kinase (Xingquan, L., et al., in Mol. Cell. Biol. (1993) 13:5225-5232), dynamin (Gout, I., et al., in Cell (1993) 75:25-36), AFAP-110 (Flynn, D. C., et al., in Mol. Cell. Biol. (1993) 13:7892-7900), and CD42 (Barfod, E. T., et al., in J. Biol. Chem. (1993) 268:26059-26062). These proteins tend to possess short, proline-rich stretches of amino acids, some of which have been directly implicated in SH3 binding. A variety of consensus sequences have been proposed, although the similarity among proline-rich regions of different SH3-binding proteins tends to be fairly low. Also, attempts to build consensus sequences are likely complicated by the incorporation of data from proteins that bind different SH3 domains.
Thus, Cicchetti, P., et al., in Science (1992) 257:803-806, published their work relating to the isolation and sequencing of two naturally-occurring proteins that could be bound in vitro by the SH3 domain of the ab1 Oncogene product. These workers found that SH3 domains bind short, proline-rich regions of such proteins. Subsequently, this same group disclosed further results (Ren, R. et al., supra) in which the SH3 binding sites of the SH3 binding proteins were localized to xe2x80x9ca nine- or ten-amino acid stretch rich in proline residues.xe2x80x9d A consensus sequence incorporating the features of the SH3 binding sites of four SH3 binding proteins was proposed: XPXXPPP¥XP (SEQ ID NO:1), wherein X indicates a position in the amino acid sequence which is not conserved among the four SH3 binding proteins, P represents proline, and ¥ indicates a hydrophobic amino acid residue, such as P or L.
The screening of complex random peptide libraries has been used to identify peptide epitopes for monoclonal (Scott, J. K. and Smith, G. P. in Science (1990) 249:386-390) and polyclonal (Kay, B. K., et al., in Gene (1993) 128:59-65) antibodies, as well as peptide ligands for a variety of proteins, including streptavidin (Devlin, J. J., et al., in Science (1990) 249:404-406; and Lam, K., et al., in Nature (1991) 354:82-84), the endoplasmic reticulum chaperone BiP (Blond-Elguindi, S., et al., in Cell (1993) 75:717-728), and CaM (Dedman, J. R., et al., in J. Biol. Chem. (1993) 268:23025-23030).
Recently, Chen, J. K. et al., in J. Am. Chem. Soc. (1993) 115:12591-12592, described ligands for the SH3 domain of phosphatidylinositol 3-kinase (PI-3xe2x80x2 Kinase) which were isolated from a biased combinatorial library. A xe2x80x9cbiasedxe2x80x9d library is to be distinguished from a xe2x80x9crandomxe2x80x9d library in that the amino acid residue at certain positions of the synthetic peptide are fixed, i. e., not allowed to vary in a random fashion. Indeed, as stated by these research workers, screening of a xe2x80x9crandomxe2x80x9d combinatorial library failed to yield suitable ligands for a PI-3xe2x80x2 Kinase SH3 domain probe. The binding affinities of these unsuitable ligands was described as weak,  greater than 100 xcexcM, based on dissociation constants measured by the Biosensor System (BIAcore).
More recently, Yu, et al. (Yu, H., et al., in Cell (1994) 76:933-945) used a xe2x80x9cbiasedxe2x80x9d synthetic peptide library of the form XXXPPXPXX (SEQ ID NO:2), wherein X represents any amino acid other than cysteine, to identify a series of peptides which bind the Src and PI-3xe2x80x2 Kinase SH3 domains. The bias was accomplished by fixing the proline residues at the specific amino acid positions indicated for the xe2x80x9crandomxe2x80x9dpeptide. As stated previously, without this bias, the technique disclosed fails to identify any SH3 domain-binding peptides.
A consensus sequence, based on 13 binding peptides was suggested: RXLPPRPXX (SEQ ID NO:3), where X tends to be a basic residue (like R, K or H). The binding affinities of several SH3 binding peptides were disclosed as ranging from 8.7 to 30 xcexcM. A xe2x80x9ccompositexe2x80x9d peptide, RKLPPRPRR (SEQ ID NO:4), was reported to have a binding affinity of 7.6 xcexcM. This value compares favorably to the binding affinity of the peptide, VPPPVPPRRR (SEQ ID NO:5), to the N-terminal SH3 domain of Grb2. See, Kraulis, P. J. J. Appl. Crystallogr. (1991) 24:946. Recognizing the limitations of their technique, Chen and co-workers, supra, stated that their results xe2x80x9cillustrate the utility of biased combinatorial libraries for ligand discovery in systems where there is some general knowledge of the ligand-binding characteristics of the receptorxe2x80x9d (emphasis added).
Yu and co-workers, supra, further described an SH3 binding site consensus sequence, XpØPpXP (SEQ ID NO:6), wherein X represents non-conserved residues, Ø represents hydrophobic residues, P is proline, and p represents residues that tend to be proline. A consensus motif of RXLPPRPXX (SEQ ID NO:7), where X represents any amino acid other than cysteine, was proposed for ligands of PI-3xe2x80x2 Kinase SH3 domain. A consensus motif of RXLPPLPRxcfx86 (SEQ ID NO:8), where xcfx86 represents hydrophobic residues, was proposed for ligands of Src SH3 domain. Still, the dissociation constants reported for the 9-mer peptides ranged only from about 8-70 xcexcM and selectivity between one type of SH3 domain and another was relatively poor, the KDs differing by only about a factor of four.
Hence, there remains a need to develop techniques for the identification of Src SH3 binding peptides which do not rely on such xe2x80x9cbiasedxe2x80x9d combinatorial peptide libraries that are limited to a partially predetermined set of amino acid sequences. Indeed, the isolation of SH3 binding peptides from a xe2x80x9crandomxe2x80x9d peptide library has not been achieved successfully before now. Furthermore, particular peptides having much greater binding affinities, whether general or more selective binding for specific SH3 domains, remain to be identified. Binding peptides specific for particular SH3 domains are useful, for example, in modulating the activity of a particular SH3 domain-containing protein, while leaving others bearing an SH3 domain unaffected. Still, the more promiscuous general binding peptides are useful for the modulation of a broad spectrum of SH3 domain-containing proteins.
The present invention relates to such SH3 binding peptides, methods for their identification, and compositions comprising same. In particular, peptides comprising particular sequences of amino acid residues are disclosed which were isolated from random peptide libraries. In the present invention, clones were isolated from a phage-displayed random peptide library which exhibited strong binding affinities for SH3 domain-containing protein targets. Some of these protein targets, include Abl, Src, Grb2, PLC-xcex4, PLC-xcex3, Ras GAP, Nck, and p85 PI-3xe2x80x2 Kinase. From the nucleotide sequence of the binding phage, the amino acid sequence of the peptide inserts has been deduced. Synthetic peptides having the desired amino acid sequences are shown to bind the SH3 domain of the target proteins. In particular, synthetic peptides combining a core consensus sequence and additional amino acid residues flanking the core sequence are especially effective at binding to particular target protein SH3 domains. The SH3 binding peptides disclosed herein can be utilized in a number of ways, including the potential modulation of oncogenic protein activity in vivo. These peptides also serve as useful leads in the production of peptidomimetic drugs that. modulate a large class of proteins involved in signal transduction pathways and oncogenesis.
Accordingly, three phage-displayed random peptide libraries were screened for isolates that bind to bacterial fusion proteins consisting of the Src homology region 3 (SH3) and glutathione S-transferase (GST). DNA sequencing of the isolates showed that they contained sequences that resemble the consensus motif, RPLPPLP (SEQ ID NO:9), within their 8, 22, or 36 amino acid long random regions. When peptides were synthesized corresponding to the pIII inserts of the SH3-binding phage, they bound to the GST fusions of the SH3 domains of Src and the Src-related proteins, such as Yes, but not of Grb2, Crk, Abl, or PLCxcex31. The synthesized peptides bind quite well to the Src SH3 domain and act as potent competitors of natural Src SH3 interactions in cell lysates. For instance, these peptides can compete with radiolabelled proteins from cell lysates in binding to immobilized Src-GST, with an apparent IC50 of 1-10 xcexcM. When a peptide, bearing the consensus sequence RPLPPLP (SEQ ID NO:9) was injected into Xenopus laevis oocytes, it accelerated the rate of progesterone-induced maturation. These results demonstrate the utility of phage-displayed random peptide libraries in identifying SH3-binding peptide sequences and that such identified peptides exhibit both in vivo and in vitro biological activity.
Thus, it is an object of the present invention to provide peptides having at least nine and up to forty-five amino acid residues, including an amino acid sequence. of the formula, R-2-L-P-5-6-P-8-9 (SEQ ID NO:10), positioned anywhere along the peptide, in which each number represents an amino acid residue, such that 2 represents any amino acid residue except cysteine, 5 and 6 each represents a hydrophobic amino acid residue, 8 represents any amino acid residue except cysteine, and 9 represents a hydrophilic amino acid residue except cysteine, each letter being the standard one-letter symbol for the corresponding amino acid, said peptide exhibiting a binding affinity for the SH3 domain of Src, provided that said peptide is not R-P-L-P-P-L-P-T-S (SEQ ID No:11). In a particular embodiment of the present invention, the peptides also exhibit a binding affinity for the SH3 domain of Src-related proteins, including Yes, Fyn, Lyn, Lck, Hck and Fgr.
The present invention also contemplates SH3 domain-binding peptides that further comprise a C-terminal-flanking amino acid sequence of the formula 10, 10-11, 10-11-12, 10-11-12-13 (SEQ ID NO:12) or 10-11-12-13-14 (SEQ ID NO:13), in which each number represents any amino acid residue except cysteine, such that 10 is bound to 9 by a peptide bond. Furthermore, peptides are also provided which further comprise an N-terminal-flanking amino acid sequence of the formula 1xe2x80x2, 2xe2x80x2-1xe2x80x2, 3xe2x80x2-2xe2x80x2-1xe2x80x2 or 4xe2x80x2-3xe2x80x2-2xe2x80x2-1xe2x80x2 (SEQ ID NO:14) in which each number represents any amino acid residue except cysteine, such that 1xe2x80x2 is bound to R by a peptide bond.
Thus, in a particular embodiment, a peptide is disclosed having at least thirteen and up to forty-five amino acid residues, including an amino acid sequence of the formula, 3xe2x80x2-2xe2x80x2-1xe2x80x2-R-2-L-P-5-6-P-8-9-10 (SEQ ID NO:15), positioned anywhere along the peptide, in which each number represents an amino acid residue, such that 3xe2x80x2, 2xe2x80x2, 1xe2x80x2, 2, 8, and each represents any amino acid residue except cysteine, 5 and 6 each represents a hydrophobic amino acid residue, and 9 represents a hydrophilic amino acid residue except cysteine, each letter being the standard one-letter symbol for the corresponding amino acid, said peptide exhibiting a binding affinity for the SH3 domain of Src.
The present invention also seeks to provide new consensus sequences or motifs that reflect variations in SH3 domain binding selectivities or specificities. The present invention also contemplates conjugates of the SH3 binding-peptides and a second molecule or chemical moiety. This second molecule may be any desired substance whose delivery to the region of the SH3 domain of a particular protein (or cell containing the protein) is sought. Possible target cells include, but are not limited to, neural cells, immune cells (e.g., T cells, B cells, natural killer cells, and the like), osteoclasts, platelets, epidermal cells, and the like, which cells express Src, Src-related proteins, and potentially, other SH3 domain-containing proteins. In this manner, the modulation of the biological activity of proteins bearing an SH3 domain can be accomplished.
Other methods and compositions consistent with the objectives of the present invention are likewise disclosed. In particular, a method is disclosed of modulating the activity of Src or Src-related proteins comprising administering a composition comprising an effective amount of a peptide of the present invention and a carrier, preferably a pharmaceutically acceptable carrier. In a specific embodiment, the contemplated method results in the inhibition of the activity of Src or Src-related proteins. Alternatively, the method is effective to activate Src or Src-related proteins.
In yet another embodiment, a method is disclosed of identifying a peptide having a region that binds to an SH3 domain comprising: (a) providing an immobilized target protein comprising an SH3 domain; (b) incubating the immobilized target protein with an aliquot taken from a random peptide library; (c) washing unbound library peptides from the immobilized target protein; (d) recovering the peptide bound to the immobilized target protein; and (e) determining the primary sequence of the SH3 domain-binding peptide.
Moreover, a method is disclosed of imaging cells, tissues, and organs in which Src or Src-related proteins are expressed, which comprises administering an effective amount of a composition comprising an SH3 domain-binding peptide conjugated to detectable label or an imaging agent.
Other objectives of the present invention will become apparent to one of ordinary skill in the art after consideration of the above disclosure and the following detailed description of the preferred embodiments.
The invention also provides assays for identifying a compound that affects the binding between a first molecule comprising an SH3 domain and a second molecule that binds to the SH3 domain comprising incubating one or more candidate compounds from which it is desired to select such a compound with the first molecule and the second molecule under conditions conducive to binding and detecting the one or more compounds that affect binding of the first molecule to the second molecule.
Also provided are kits for performing such assays comprising a first molecule comprising an SH3 domain and a second molecule that binds to the SH3 domain.